Morse warned that there was ‘little flexibility’ in the government’s plans for a new customs system after Brexit.
Photograph: Geert Vanden Wijngaert/AP

A lack of energy and leadership in Theresa May’s government has left hopes of a successful Brexit at risk of falling apart “like a chocolate orange”, a leading government watchdog has warned.

In an extraordinary intervention that will raise the pressure on the prime minister to reassess her approach to Brexit, the comptroller and auditor general of the National Audit Office said the government had failed to take a unified approach to talks with the EU. He also revealed that a request to see a ministerial plan for the changes needed to leave the EU had been met with only “vague” assurances.

Amyas Morse said that the result could be failures across Whitehall as the negotiations unfold. “Can government actually step up in these very difficult circumstances and deliver a unified response?” he asked. “I’m not seeing it yet.”

Morse, whose role as chief auditor gives him a statutory responsibility to scrutinise all public spending, has spoken out in a rare interview with reporters – a reflection of his growing concern. He suggested that the Department for Exiting the EU (DExEU), the Treasury and the cabinet office had so far failed to take an “energetic” lead, leaving other departments to set their own priorities.

“These options could have been activated by now. The combined forces of DExEU leadership, Treasury and Cabinet Office should be speaking on one voice on these matters,” he said.

He said he has asked to see, but not been shown, a ministerial plan to guide government departments through structural and legal changes for the UK to leave the EU. He had only received “vague” assurances that the government would support struggling departments trying to enact complex and expensive changes made necessary by Brexit, he said.

Morse’s alarming verdict comes as the National Audit Office said there was “very little flexibility” in plans for a new customs system, which is due to be ready two months before Britain is supposed to leave the EU.

“Leaving the EU is a negotiation,” Morse said. “It means the results are uncertain and [departments] need to be fast and flexible and react in a unified way. We have an issue there because we have departmental government. What we don’t want to find is that at the first tap it falls apart like a chocolate orange. It needs to be coming through like a cricket ball,” he said.

“There has to be strong integration. To have things start to go wrong and then say, ‘Oops, perhaps we might have to be a bit better integrated’ really is second best.”

There could be hundreds of new projects launched by government departments and hundreds of project managers recruited to help implement Brexit, as well as more than a thousand statutory instruments passed, he said.

Morse said he had “expressed interest” to both the Brexit secretary, David Davis, and Oliver Robbins, the department’s permanent secretary, that he would like to see a cross-departmental plan on Brexit implementation. Neither had so far put one forward, he indicated.

Asked what DExEU’s response was, he responded with a single word: vague. He added that he “wouldn’t be speaking like this” if he believed the coordinated support needed across government to deal with Brexit was in place. “It is symptomatic of whether the government is really able to drive this across departments or whether we leave each department to struggle with it on their own.

“We want to see a more unified approach. That is very much from the point of protecting UK taxpayers’ interests – it is not because of anything else,” he said.

Last summer, Morse told the Guardian that billions of pounds’ worth of projects should be scrapped by May because of a “tidal wave” of pressures from an impending Brexit. So far, his warnings have gone unheeded, and he reiterated the need for the government to re-examine major projects.

Turning to the report into the new customs declaration service, which is being updated for Brexit, he warned that it would be a “horror show” if officials were forced to manually process imports and exports. HM Revenue and Customs (HMRC) estimates that the number of annual customs declarations will rise from 55 million to 255 million after March 2019.

The new system for processing imports and exports, which was signed off before the referendum vote, is expected to be completed just two months before the Brexit deadline of March 2019.

The report said it was unreasonable to leave HMRC to decide whether more money and resources should be spent on ensuring that there was a working system in place on day one of the UK’s future outside the EU.

Although customs reforms were progressing, there was normally a drift in the timescale of major IT projects, he said. “The reason for emphasising these points is the government really needs to recognise that. I’ve noticed in some of the public comments it is starting to lay off on the risk a little bit.”

Contingency plans have been outlined in case of delays in the CDS being introduced, but they were not well developed, the watchdog said. In the worst case, customs officials could revert to manual processing at border points, but “that would be a bit of a horror show”, Morse said.

An HMRC spokesman said: “The Customs Declaration Service is on track for delivery by January 2019 and will support international trade once the UK leaves the European Union.”